Thanks Doug, i downloaded it and now the file exists: $FREESURFER_HOME/bin/fslmaths.fsl
Unfortuantely it is still not running and gives the same error when running preproc-sess: mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0 ERROR: cannot find either fslmaths for avwmaths How can i proceed? Thanks, Eiran ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, April 02, 2014 12:41 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] preprocessing question thanks, it must be something in our distribution script affecting mac On 04/01/2014 05:13 PM, Markus Gschwind wrote: > Thanks Doug, > > I notice that on my Mac > build freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 > > ...I don't have fslmaths.fsl neither. There are only > > $ which $FREESURFER_HOME/bin/fsl* > /Applications/freesurfer/bin/fsl_label2voxel > /Applications/freesurfer/bin/fsl_rigid_register > /Applications/freesurfer/bin/fsl_sub_mgh > /Applications/freesurfer/bin/fslregister > > $ which $FREESURFER_HOME/bin/*.fsl > /Applications/freesurfer/bin/epidewarp.fsl > /Applications/freesurfer/bin/fscalc.fsl > /Applications/freesurfer/bin/mri_motion_correct.fsl > > (I never executed the above mentioned process of Eiran thoug...) > > Best, > Markus > > > > > > 2014-04-01 18:36 GMT+02:00 Douglas N Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>: > > That is weird. You can get a copy from here > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fslmaths.fsl.mac > > copy it to > > $FREESURFER_HOME/bin/fslmaths.fsl > > > On 04/01/2014 12:25 PM, Eiran Harel wrote: > > Hi Doug, > > No, it does not exist. > > What should i do? > > Thanks, > > Eiran > > ________________________________________ > > From: freesurfer-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > [freesurfer-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of > Douglas N Greve [gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>] > > Sent: Tuesday, April 01, 2014 7:16 PM > > To: freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > Subject: Re: [Freesurfer] preprocessing question > > > > does $FREESURFER_HOME/bin/fslmaths.fsl exist? > > > > On 04/01/2014 03:59 AM, Eiran Harel wrote: > >> Dear freesurfers, > >> I have installed freesurfer and fsl on my Mac: > >> * > >> * > >> *-------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 > --------* > >> *Setting up environment for FreeSurfer/FS-FAST (and FSL)* > >> *FREESURFER_HOME /Applications/freesurfer* > >> *FSFAST_HOME /Applications/freesurfer/fsfast* > >> *FSF_OUTPUT_FORMAT nii.gz* > >> *SUBJECTS_DIR /Applications/freesurfer/subjects* > >> *MNI_DIR /Applications/freesurfer/mni* > >> *FSL_DIR /usr/local/fsl* > >> > >> I am trying to run Preproc-sess command: > >> > >> *preproc-sess -s bsmt102 -surface fsaverage lhrh -mni305 -fwhm > 5 -fsd > >> bold -stc odd -per-run -force* > >> > >> and get this error: > >> > >> *mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 > >> -ndil 1 -nerode 0* > >> *ERROR: cannot find either fslmaths for avwmaths* > >> * > >> * > >> Any suggestions? > >> Thanks! > >> Eiran > >> > >> > >> > >> > >> <http://www.tasmc.org.il/be-well/Pages/default.aspx> > >> <https://www.facebook.com/ichilov.medical> > >> <http://twitter.com/tasmc1> <http://www.youtube.com/tasmc1> > >> <http://www.tasmc.org.il/sites/en/Pages/default.aspx> > >> > >> > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > Phone Number: 617-724-2358 <tel:617-724-2358> > > Fax: 617-726-7422 <tel:617-726-7422> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the person > to whom it is > > addressed. If you believe this e-mail was sent to you in error > and the e-mail > > contains patient information, please contact the Partners > Compliance HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent > to you in error > > but does not contain patient information, please contact the > sender and properly > > dispose of the e-mail. > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
